Interactions among oscillatory pathways in NF-kappa B signaling

<p>Abstract</p> <p>Background</p> <p>Sustained stimulation with tumour necrosis factor alpha (TNF-alpha) induces substantial oscillations—observed at both the single cell and population levels—in the nuclear factor kappa B (NF-kappa B) system. Although the mechanism has not yet been elucidated fully, a core system has been identified consisting of a negative feedback loop involving NF-kappa B (RelA:p50 hetero-dimer) and its inhibitor I-kappa B-alpha. Many authors have suggested that this core oscillator should couple to other oscillatory pathways.</p> <p>Results</p> <p>First we analyse single-cell data from experiments in which the NF-kappa B system is forced by short trains of strong pulses of TNF-alpha. Power spectra of the ratio of nuclear-to-cytoplasmic concentration of NF-kappa B suggest that the cells' responses are entrained by the pulsing frequency. Using a recent model of the NF-kappa B system due to Caroline Horton, we carried out extensive numerical simulations to analyze the response frequencies induced by trains of pulses of TNF-alpha stimulation having a wide range of frequencies and amplitudes. These studies suggest that for sufficiently weak stimulation, various nonlinear resonances should be observable. To explore further the possibility of probing alternative feedback mechanisms, we also coupled the model to sinusoidal signals with a wide range of strengths and frequencies. Our results show that, at least in simulation, frequencies other than those of the forcing and the main NF-kappa B oscillator can be excited via sub- and superharmonic resonance, producing quasiperiodic and even chaotic dynamics.</p> <p>Conclusions</p> <p>Our numerical results suggest that the entrainment phenomena observed in pulse-stimulated experiments is a consequence of the high intensity of the stimulation. Computational studies based on current models suggest that resonant interactions between periodic pulsatile forcing and the system's natural frequencies may become evident for sufficiently weak stimulation. Further simulations suggest that the nonlinearities of the NF-kappa B feedback oscillator mean that even sinusoidally modulated forcing can induce a rich variety of nonlinear interactions.</p

An overview of gradient-enhanced metamodels with applications

International audienceMetamodeling, the science of modeling functions observed at a finite number of points, benefits from all auxiliary information it can account for. Function gradients are a common auxiliary information and are useful for predicting functions with locally changing behaviors. This article is a review of the main metamodels that use function gradients in addition to function values. The goal of the article is to give the reader both an overview of the principles involved in gradient-enhanced metamodels while also providing insightful formulations. The following metamodels have gradient-enhanced versions in the literature and are reviewed here: classical, weighted and moving least squares, Shepard weighting functions, and the kernel-based methods that are radial basis functions, kriging and support vector machines. The methods are set in a common framework of linear combinations between a priori chosen functions and coefficients that depend on the observations. The characteristics common to all kernel-based approaches are underlined. A new ν-GSVR metamodel which uses gradients is given. Numerical comparisons of the metamodels are carried out for approximating analytical test functions. The experiments are replicable, as they are performed with an opensource available toolbox. The results indicate that there is a trade-off between the better computing time of least squares methods and the larger versatility of kernel-based approaches